6fpv
From Proteopedia
(Difference between revisions)
(New page: ==A llama-derived JBP1-targeting nanobody== <StructureSection load='6fpv' size='340' side='right' caption='6fpv, resolution 1.64Å' scene=''> == Structural highlig...) |
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<StructureSection load='6fpv' size='340' side='right' caption='[[6fpv]], [[Resolution|resolution]] 1.64Å' scene=''> | <StructureSection load='6fpv' size='340' side='right' caption='[[6fpv]], [[Resolution|resolution]] 1.64Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6fpv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FPV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FPV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6fpv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FPV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FPV FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6fpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fpv OCA], [http://pdbe.org/6fpv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fpv RCSB], [http://www.ebi.ac.uk/pdbsum/6fpv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fpv ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6fpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fpv OCA], [http://pdbe.org/6fpv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fpv RCSB], [http://www.ebi.ac.uk/pdbsum/6fpv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fpv ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | J-base binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (beta-D-glucosylhydroxymethyluracil), a modification of thymidine confined to some protozoa. Camelid (llama) single-domain antibody fragments (nanobodies) targeting JBP1 were produced for use as crystallization chaperones. Surface plasmon resonance screening identified Nb6 as a strong binder, recognizing JBP1 with a 1:1 stoichiometry and high affinity (Kd = 30 nM). Crystallization trials of JBP1 in complex with Nb6 yielded crystals that diffracted to 1.47 A resolution. However, the dimensions of the asymmetric unit and molecular replacement with a nanobody structure clearly showed that the crystals of the expected complex with JBP1 were of the nanobody alone. Nb6 crystallizes in space group P31 with two molecules in the asymmetric unit; its crystal structure was refined to a final resolution of 1.64 A. Ensemble refinement suggests that in the ligand-free state one of the complementarity-determining regions (CDRs) is flexible, while the other two adopt well defined conformations. | ||
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| + | Characterization and structure determination of a llama-derived nanobody targeting the J-base binding protein 1.,van Beusekom B, Heidebrecht T, Adamopoulos A, Fish A, Pardon E, Steyaert J, Joosten RP, Perrakis A Acta Crystallogr F Struct Biol Commun. 2018 Nov 1;74(Pt 11):690-695. doi:, 10.1107/S2053230X18010282. Epub 2018 Oct 16. PMID:30387773<ref>PMID:30387773</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6fpv" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Camelus glama]] | ||
[[Category: Adamopoulos, A]] | [[Category: Adamopoulos, A]] | ||
[[Category: Beusekom, B van]] | [[Category: Beusekom, B van]] | ||
Current revision
A llama-derived JBP1-targeting nanobody
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